Double auxotrophic mycobacterium and uses thereof

ABSTRACT

Provided are attenuated strains of M. tuberculosis and M. bovis BCG which are double auxotrophic mutants with genes knocked out in the biosynthetic pathways for arginine and methionine, and compositions and methods of use thereof.

STATEMENT OF GOVERNMENT SUPPORT

This invention was made with government support under grant numbers A1026170 awarded by the National Institutes of Health. The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

Tuberculosis (TB), a disease that globally kills 1.7 million people each year, is a major health problem. The situation is further worsened by emergence of multi-drug resistant (MDR) strains, extensively drug resistant (XDR) strains, and HIV co-infections. The rise in resistant Mycobacterium tuberculosis (Mtb) strains and HIV co-infections demands new vaccines and/or drug treatments. The only available vaccine against TB is the Bacillus Calmette-Guérin (BCG) vaccine, however, the BCG vaccine provides limited protection against pulmonary tuberculosis in adults. Moreover, the BCG vaccine has variable efficacy against Mtb, depending on the geographical region. Additionally, the failure of TB vaccine candidate testing in clinical trials is an economic burden as the clinical trials are expensive and only a few candidates can be tested at one time. Additionally, there is no safe human TB challenge model available to evaluate the efficacy of vaccine candidates against TB.

The disclosures of all publications, patents, patent application publications and books referred to herein, are hereby incorporated by reference in their entirety into the subject application to more fully describe the art to which the subject invention pertains.

SUMMARY OF THE INVENTION

Provided is an auxotrophic mycobacterium comprising a mycobacterial genome in which (i) a gene encoding an enzyme essential in an arginine synthesis pathway has been fully or partially deleted and (ii) a gene encoding an enzyme essential in a methionine synthesis pathway has been fully or partially deleted.

Also provided is a composition comprising an auxotrophic mycobacterium with a mycobacterial genome in which (i) a gene (s) encoding an enzyme essential in an arginine synthesis pathway has been fully or partially deleted and (ii) a gene(s) encoding an enzyme essential in a methionine synthesis pathway has been fully or partially deleted, and a carrier.

Also provided is a method of eliciting an immune response in a subject comprising administering to the subject the composition or vaccine described herein in an amount effective to elicit an immune response.

Also provided is a method of vaccinating a subject comprising administering to the subject the composition or vaccine described herein in an amount effective to vaccinate a subject.

Also provided is a method of treating a subject for tuberculosis comprising administering to the subject the composition or vaccine described herein in an amount effective to treat a subject.

Also provided is a method of treating a subject for a cancer comprising administering to the subject the composition or vaccine described herein in an amount effective to treat a subject.

Also provided is a method of determining the efficacy of a candidate tuberculosis vaccine, comprising: administering the candidate tuberculosis vaccine to an animal which has been infected with the auxotrophic mycobacterium described herein, quantifying the amount of auxotrophic mycobacterium in the animal at one or more time points subsequent to administering the candidate tuberculosis vaccine, and comparing the amount of auxotrophic mycobacterium quantified to a predetermined control amount, or to the amount of auxotrophic mycobacterium infected into the animal, so as to determine the efficacy of the candidate tuberculosis vaccine.

Also provided is a method of determining the efficacy of a candidate small organic molecule tuberculosis treatment, comprising: administering the small organic molecule tuberculosis treatment to an animal which has been infected with the auxotrophic mycobacterium described herein, quantifying the amount of auxotrophic mycobacterium in the animal at one or more time points subsequent to administering the candidate tuberculosis vaccine, and comparing the amount of auxotrophic mycobacterium quantified to a predetermined control amount, or to the amount of auxotrophic mycobacterium infected into the animal, so as to determine the efficacy of the small organic molecule tuberculosis treatment.

BRIEF DESCRIPTION OF THE DRAWINGS

The above and other advantages and features of this disclosure will become more apparent by describing in further detail exemplary embodiments thereof with reference to the accompanying drawings.

FIG. 1A is a graph of percent survival versus time (days) for severe combined immunodeficiency (SCID) mice intravenously infected with H37Rv (wild type (WT), virulent Mtb strain, black circles) or Mtb strain ΔargBΔmetA (open circles), at a dose of 10⁸ bacilli/mice.

FIGS. 1B to 1D are graphs of colony forming units (CFU) per tissue versus time (days), showing the sterilization of Mtb strain ΔargBΔmetA in the lung (FIG. 1B), liver (FIG. 1C), and spleen (FIG. 1D) of SCID mice infected by intravenous route with 10⁶ bacilli/mouse.

FIGS. 2A, 2B, and 2C are graphs of CFU/lung versus time (days) as detected in aerosol infected C57BL/6 mice (FIG. 2A), interferon gamma (IFN-γ) knock out mice (FIG. 2B) and inducible nitric oxide synthase (iNOS) knockout mice (FIG. 2C).

FIG. 3 is a graph of CFU/ml versus time (days) showing the growth of strain mc²8398 in arginine and methionine free media (mc²8398⁻) and in arginine and methionine containing media (mc² 8398⁺).

FIG. 4A is a graph of percent survival versus number of days showing the survival of strain mc²8398 in SCID mice.

FIGS. 4B, 4C, and 4D are graphs of CFU per tissue versus time (weeks), showing the decrease in CFU over time in the lung (FIG. 4B), liver (FIG. 4C), and spleen (FIG. 4D) of SCID mice infected by the intravenous route with 10⁶ bacilli/mouse of strain mc²8398.

FIGS. 5A, 5B, and 5C are graphs of CFU per tissue versus time (weeks), showing the decrease in CFU over time in the lung (FIG. 5A), spleen (FIG. 5B), and liver (FIG. 5C) of immunocompromised Rag^(−/−) mice infected by intravenous route with strains H37Rv, CDC1551, mc²8392, and mc²8398 at a dose of 10⁶ bacilli/mouse.

FIGS. 6A, 6B, and 6C are graphs of CFU per tissue versus time (weeks), showing the decrease in CFU over time in the lung (FIG. 5A), spleen (FIG. 5B), and liver (FIG. 5C) of immunocompromised Rag^(−/−) mice infected by intravenous route with strains H37Rv, CDC1551, mc²8392, mc²8398, mc²7901, and mc²7902 at a dose of 10⁶ bacilli/mouse.

FIG. 7 is a diagram illustrating the immunization and challenge schedule of an experiment designed to evaluate the efficacy of strain mc²8398 to protect against challenge with wild type Mycobacterium tuberculosis strain H37Rv, by different routes of immunization.

FIG. 8A is a graph of CFU per lung versus number of weeks post challenge with virulent Mycobacterium tuberculosis H37Rv and FIG. 8B is a graph of CFU per spleen versus number of weeks post challenge with virulent Mycobacterium tuberculosis H37Rv.

FIG. 9 is a diagram illustrating the immunization and challenge schedule of an experiment designed to evaluate the efficacy of Mtb strain ΔargBΔmetA against wild type Mycobacterium tuberculosis strain H37Rv by different routes of immunization.

DETAILED DESCRIPTION

Provided is a mycobacterium comprising a mycobacterial genome in which (i) at least one gene encoding an enzyme essential in an arginine synthesis pathway has been fully or partially deleted and (ii) at least one gene encoding an enzyme essential in a methionine synthesis pathway has been fully or partially deleted. The mycobacterium is thus an auxotrophic mycobacterium, and more specifically, is a double deletion mutant that is auxotrophic for methionine and arginine.

In embodiments, the auxotrophic mycobacterium is incapable of synthesizing arginine and methionine.

In embodiments, the auxotrophic mycobacterium prior to the full or partial gene deletions of a gene encoding an enzyme essential in an arginine synthesis pathway and a gene encoding an enzyme essential in a methionine synthesis pathway is a Mycobacterium tuberculosis.

In embodiments, the auxotrophic mycobacterium prior to the full or partial gene deletions of a gene encoding an enzyme essential in an arginine synthesis pathway and a gene encoding an enzyme essential in a methionine synthesis pathway is a Mycobacterium bovis Bacillus Calmette-Guérin.

The auxotrophic mycobacterium can comprise a mycobacterial genome in which a single gene encoding an enzyme essential in an arginine synthesis pathway is fully or partially deleted from the mycobacterial genome or can comprise a mycobacterial genome in which more than one (e.g., 2, 3, 4, etc.) gene encoding an enzyme essential in an arginine synthesis pathway can be fully or partially deleted from the mycobacterial genome. Similarly, the auxotrophic mycobacterium can comprise a mycobacterial genome in which a single gene encoding an enzyme essential in an methionine synthesis pathway is fully or partially deleted from the mycobacterial genome or can comprise a mycobacterial genome in which more than one (e.g., 2, 3, 4, etc.) gene encoding an enzyme essential in an methionine synthesis pathway can be fully or partially deleted from the mycobacterial genome.

In embodiments, the gene encoding an enzyme essential in an arginine synthesis pathway comprises an argA gene, an argB gene, an argE gene, an argF gene, or a combination thereof, or is an equivalent to the Mycobacterium tuberculosis gene, i.e. a gene which encodes an ArgA, ArgB, argE, argF enzyme in another Mycobacterium strain. The argA gene is a gene encoding a mycobacterial amino acid acetyltransferase ArgA enzyme, the argB gene is a gene encoding a mycobacterial acetylglutamate kinase ArgB enzyme, the argE gene is a gene encoding a mycobacterial acetylornithine deacteylase ArgE enzyme, and the argF gene is a gene encoding a mycobacterial ornithine carbamoyltransferase ArgF enzyme. In embodiments, the gene encoding an enzyme essential in an arginine synthesis pathway is a gene encoding a mycobacterial acetylglutamate kinase ArgB enzyme. For example, the argB gene is a gene encoding UniProtKB—P9WQ01 (ARGB_MYCTU).

In embodiments, the gene encoding an enzyme essential in a methionine synthesis pathway is comprises a metA gene, a metC gene, a metD gene, a metE gene, and a metF gene, or a combination thereof, or is an equivalent to the Mycobacterium tuberculosis gene, i.e., a gene which encodes a MetA enzyme in another Mycobacterium strain. The metA gene is a gene encoding homoserine O-acetyltransferase MetA enzyme, the metC gene is a gene encoding a mycobacterial cystathionine β-lyase MetC enzyme, the metE gene is a gene encoding a mycobacterial cobalamin-independent methionine synthase MetE enzyme, and the metF gene is a gene encoding a mycobacterial methylenetetrahydrofolate reductase MetF enzyme. In embodiments, the gene encoding an enzyme essential in a methionine synthesis pathway is a metA gene encoding a mycobacterial homoserine O-acetyltransferase MetA enzyme. In embodiments, the gene encoding an enzyme essential in a methionine synthesis pathway is a Mycobacterium tuberculosis gene encoding a mycobacterial homoserine O-acetyltransferase MetA enzyme.

In embodiments, the auxotrophic mycobacterium comprises a mycobacterial genome in which at least one of an argA gene, an argB gene, an argE gene, an argF gene, or a combination thereof is fully or partially deleted and at least one of a metA gene, a metC gene, a metD gene, a metE gene, and a metF gene, or a combination thereof is fully or partially deleted.

In embodiments, the auxotrophic mycobacteria comprises a mycobacterial genome in which at least one gene encoding a homoserine O-acetyltransferase MetA enzyme and an acetylglutamate kinase ArgB enzyme are fully or partially deleted. That is, the auxotrophic mycobacteria has a full or partial deletion of at least one gene encoding a homoserine O-acetyltransferase MetA enzyme and a full or partial deletion of at least one gene encoding a acetylglutamate kinase ArgB enzyme.

In embodiments, the auxotrophic mycobacterium prior to the full or partial gene deletions of a gene encoding an enzyme essential in an arginine synthesis pathway and a gene encoding an enzyme essential in a methionine synthesis pathway is an H37Rv Mycobacterium tuberculosis strain. In an embodiment, the H37Rv Mycobacterium tuberculosis strain (i.e. a mycobacterium prior to deletion of the relevant genes) is deposited with the American Type Culture Collection (ATCC) as Accession No. ATCC27294. In embodiments, the auxotrophic mycobacterial genome prior to the full or partial gene deletions of a gene encoding an enzyme essential in an arginine synthesis pathway and a gene encoding an enzyme essential in a methionine synthesis pathway is a H37Rv Mycobacterium tuberculosis genome. In embodiments, the auxotrophic mycobacterial genome prior to the full or partial gene deletions of a gene encoding an enzyme essential in an arginine synthesis pathway and a gene encoding an enzyme essential in a methionine synthesis pathway is a H37Rv Mycobacterium tuberculosis Bacillus Calmette-Guérin. In an embodiment, the Mycobacterium tuberculosis Bacillus Calmette-Guérin (i.e. a mycobacterium prior to deletion of the relevant genes) is deposited with the ATCC as Accession No. ATCC 35737.

Also provided is a composition comprising an auxotrophic mycobacterium comprising a mycobacterial genome in which (i) a gene encoding an enzyme essential in an arginine synthesis pathway has been fully or partially deleted and (ii) a gene encoding an enzyme essential in a methionine synthesis pathway has been fully or partially deleted, and a carrier.

In embodiments, the composition is a vaccine. In embodiments, the composition further comprises an immunologic adjuvant.

To facilitate growth in vitro, the auxotrophic mycobacterium is grown in liquid or solid culture media which is supplemented with an amount of arginine and an amount of methionine. Accordingly, in embodiments, the composition comprises an amount of arginine, an amount of methionine, or a combination thereof. In embodiments, the composition comprises an amount of arginine and an amount of methionine.

In embodiments, the composition comprises an amount of arginine biosynthetic gene, an amount of methionine biosynthetic gene, or a combination thereof. In embodiments, the composition comprises an amount of the arginine biosynthetic gene and an amount of the methionine biosynthetic gene.

Optionally, the auxotrophic mycobacterium can be separated from the growth media and washed to remove residual traces of the media from the mycobacterial cells. Accordingly, in embodiments, the composition does not comprise arginine, methionine, or a combination thereof. For example, the composition does not comprise arginine, or the composition does not comprise methionine, or the composition does not comprise arginine and methionine.

In embodiments, the auxotrophic mycobacterium further comprises a reporter gene insertion in the mycobacterial genome thereof and wherein the amount of auxotrophic mycobacterium in the animal at one or more time points is quantified by quantifying a reporter signal. For example, a plasmid encoding a reporter gene can be used to insert the reporter gene in the mycobacterial genome of the auxotrophic mycobacterium. The reporter gene can be a gene encoding a protein which when expressed, can be used to detect the presence of the auxotrophic mycobacterium in vivo. Examples of the reporter gene include, but are not limited to, a luciferase gene (e.g., NanoLuc®), a green fluorescent protein (GFP) gene, a red fluorescent protein (RFP) gene, a near-infrared fluorescent protein (iRFP) gene, and a tyrosinase gene.

Also provided is a method of eliciting an immune response in a subject, the method comprising administering to the subject the composition or vaccine described herein in an amount effective to elicit an immune response.

Also provided is a method of vaccinating a subject comprising administering to the subject an amount of the composition or vaccine described herein in an amount effective to vaccinate a subject.

Also provided is a method of treating a subject for tuberculosis comprising administering to the subject the composition or vaccine described herein in an amount effective to treat a subject.

In embodiments, the subject has pulmonary tuberculosis.

In embodiments, the tuberculosis is pulmonary tuberculosis.

In embodiments, the subject has tuberculosis meningitis.

In embodiments, the tuberculosis is tuberculosis meningitis.

Also provided is a method of treating a subject for a cancer comprising administering to the subject the composition or vaccine described herein in an amount effective to treat a subject.

In embodiments, the cancer is a genitourinary cancer.

In embodiments, the cancer is a non-invasive bladder cancer.

In embodiments, the amount of the composition is administered into (e.g., directly into) the bladder of the subject via a catheter.

In embodiments, the subject is immunocompromised.

In embodiments of the methods, the subject is human.

In embodiments of the methods, the auxotrophic mycobacterial genome comprises no additional gene deletions.

Also provided is a method of determining the efficacy of a candidate tuberculosis vaccine, comprising: administering the candidate tuberculosis vaccine to an animal which has been infected with the auxotrophic mycobacterium described herein, quantifying the amount of auxotrophic mycobacterium in the animal at one or more time points subsequent to administering the candidate tuberculosis vaccine, and comparing the amount of auxotrophic mycobacterium quantified to a predetermined control amount, or to the amount of auxotrophic mycobacterium infected into the animal, so as to determine the efficacy of the candidate tuberculosis vaccine.

Also provided is a method of determining the efficacy of a candidate small organic molecule tuberculosis treatment, comprising: administering the small organic molecule tuberculosis treatment to an animal which has been infected with the auxotrophic mycobacterium described herein, quantifying the amount of auxotrophic mycobacterium in the animal at one or more time points subsequent to administering the candidate tuberculosis vaccine, and comparing the amount of auxotrophic mycobacterium to a predetermined control amount, or to the amount of auxotrophic mycobacterium infected into the animal, so as to determine the efficacy of the small organic molecule tuberculosis treatment.

In an embodiment of the carrier of the composition, the carrier is a pharmaceutically acceptable carrier.

In embodiments, the candidate small organic molecule tuberculosis treatment comprises a small organic molecule that is a potential candidate for treatment of disease caused by a MDR and/or XDR strain of Mycobacterium tuberculosis.

Examples of pharmaceutically acceptable carriers include, but are not limited to, phosphate buffered saline solution, sterile water (including water for injection USP), emulsions such as oil/water emulsion, and various types of wetting agents. Diluents for aerosol or parenteral administration include phosphate buffered saline or normal (0.9%) saline, for example 0.9% sodium chloride solution, USP. Compositions comprising such carriers are formulated by methods known to those of skill in the art (see, for example, Remington's Pharmaceutical Sciences, 18th edition, A. Gennaro, ed., Mack Publishing Co., Easton, Pa., 1990; and Remington, The Science and Practice of Pharmacy 20th Ed. Mack Publishing, 2000, the content of each of which is hereby incorporated in its entirety). In non-limiting examples, the carrier can comprise one or more of dibasic sodium phosphate, potassium chloride, monobasic potassium phosphate, polysorbate 80 (e.g. 2-[2-[3,5-bis(2-hydroxyethoxy)oxolan-2-yl]-2-(2-hydroxyethoxy)ethoxy]ethyl (E)-octadec-9-enoate), disodium edetate dehydrate, sucrose, monobasic sodium phosphate monohydrate, and dibasic sodium phosphate dihydrate. A combination comprising at least one of the foregoing can also be used.

“And/or” as used herein, for example, with option A and/or option B, encompasses the separate embodiments of (i) option A, (ii) option B, and (iii) option A plus option B.

All combinations of the various elements described herein are within the scope of the invention unless otherwise indicated herein or otherwise clearly contradicted by context.

This invention may be better understood from the Experimental Details, which follow.

EXPERIMENTAL DETAILS

Herein disclosed is an auxotrophic mycobacterium, which is an auxotrophic M. tuberculosis (Mtb) strain and which can be used as a vaccine, as a treatment for TB, and which can also be safely used in a human TB challenge model. This auxotrophic mycobacterium Mtb strain represents a viable candidate for human challenge trials. Unlike BCG, or the leucine or pantothenate auxotrophic mutants of either BCG or M. tuberculosis, which persist in mammals, both the Mtb methionine auxotroph ΔmetA and the Mtb arginine auxotroph ΔargB are rapidly cleared in immunocompromised mice. In contrast, the ΔargBΔmetA double auxotroph is rapidly sterilized in media without arginine and/or methionine.

The auxotrophic mycobacterium strain with a reporter gene inserted therein, would give a functional human challenge test strain. Work with M. tuberculosis requires access to a BSL3 (biosafety level 3) facility, which is cumbersome and hazardous for large-scale drug screening programs. Herein is disclosed a safe, BSL2 (biosafety level 2) auxotrophic mycobacterium strain for screening drugs against Mycobacterium tuberculosis (Mtb). The auxotrophic mycobacterium strain has the same growth rate as wild type M tuberculosis strains when cultured in supplemented media. The auxotrophic mycobacterium strain does not persist and is sterilized in both in vitro and in vivo models. As shown in FIG. 1A, severe combined immunodeficient (SCID) mice infected with an extremely high dose of 10⁸ mycobacterium, were healthy and alive even at day 300-post infection, while mice infected with the parent strain (Mtb, strain H37Rv) were dead within 10 days. Additionally, no viable bacteria and no suppressor mutants that can bypass these deletions were recovered from the SCID mice.

Additionally, the auxotrophic mycobacterium strain can replace BCG to treat tuberculous meningitis and non-invasive bladder cancers. Several cases of BCG dissemination have been reported in BCG vaccinated people undergoing organ transplants or immunosuppressive treatments for cancer. BCG cannot be used in immunocompromised patients. BCG persists, is not sterilized in a SCID mouse model, and kills mice at later time points. Meanwhile, the auxotrophic mycobacterium strain disclosed herein has been demonstrated to be extremely safe.

Amino acid auxotrophies can be either bacteriostatic or bactericidal in vivo, but are not necessarily sterilizing. In Mtb most of the studied auxotrophies are bacteriostatic, however, the arginine and methionine amino acid auxotrophies described herein are sterilizing. As used herein, the terms “sterilization” and “sterilizing” refer to the death of the microorganism, which can occur either in vivo or in vitro. For example, the arginine or methionine deprived Mtb bacillus disclosed herein dies, i.e. does not persist, when deprived of arginine or methionine. Arginine or methionine deprivation rapidly sterilizes the auxotrophic mycobacterium strain having ΔargB or ΔmetA, which is deficient in the biosynthesis pathway of the respective amino acids, without the emergence of a suppressor mutant (i.e., a mutant that can bypass the deficiency in the pathway).

Testing of the Mtb strain ΔargB and the Mtb strain ΔmetA mutant for revertance during culture showed that the reversion rate is less than 1×10⁹ cells for each mutation. Further, there is no emergence of a suppressor mutant either in vitro or in vivo in immunocompetent as well as in immunodeficient SCID mice. As shown in FIG. 1B, the auxotrophic Mtb strain ΔargBΔmetA is sterilized in the lung, liver, and spleen of SCID mice infected by the intravenous route with 10⁶ bacilli.

It was also found that auxotrophic Mtb strains deficient in de novo arginine biosynthesis pathway (ΔargB or ΔargF) are sterilized and do not persist in other tested immunodeficient (INFγ^(−/−) and phox^(−/−)) mouse models. Mice were infected by aerosol with 10⁶ bacilli of Mtb ΔargB or Mtb ΔargF. (See FIGS. 2A-2C).

In summary, auxotrophic mycobacterium strains are extremely safe, non-persistent, and acquire no bypass mutations or suppressors in vitro and in vivo. As disclosed herein, the auxotrophic mycobacterium is a double auxotrophic strain having both arginine and methionine sterilizing auxotrophies combined in a single strain. Accordingly, the auxotrophic mycobacterium is safer and non-persistent.

Methods: Gene Knockout—The gene metA or argB can be deleted, in Mtb H37Rv and M. bovis bacillus Calmette-Guérin for example, by specialized transduction as described previously (Jain et al, Specialized transduction designed for precise high-throughput unmarked deletions in Mycobacterium tuberculosis. MBio 5 (3): e01245-e14). Transductants can be recovered on selective medium, e.g. containing hygromycin and methionine (50 μg/mL). Confirmation of transduction can be obtained by, e.g., by three-primer PCR using primers and Universal uptag.

Table 1 shows various Mtb and M. bovis strains which have been constructed and/or tested.

TABLE 1 Strain no Genotype How Constructed 1 BCG SSI Danish BCG SSI Danish Jacobs Collection 2 mc²8411 ΔmetA:: hyg sacB Specialized transduction in BCG Danish using phAE783 3 mc²8412 ΔmetA mc²8411 unmarked using phAE280 4 mc²8413 ΔmetA ΔargB:: hyg sacB Specialized transduction in me²8412 with phAE773 5 BCG Tice BCG Tice Jacobs Collection 6 mc²8414 ΔmetA:: hyg sacB Specialized transduction with phAE783 in BCG Tice 7 mc²2 H37Rv Jacobs Collection 8 mc²7470 ΔargB::hyg sacB Specialized transduction of mc²2 with phAE773 9 mc²7476 ΔargB mc²7470 unmarked using phAE280 10 mc²8219 ΔargB ΔmetA::hyg sacB Specialized transduction of mc²7476 with phAE773 11 mc²8398 ΔargB ΔmetA mc²8219 unmarked using phAE280 12 mc²7680 ΔargF::hyg sacB Specialized transduction of mc²2 with phAE774 13 mc²7958 ΔargF mc²7680 unmarked using phAE280 14 mc²2600 CDC1551 Jacobs Collection 15 mc²7477 ΔargB::hyg sacB Specialized transduction of CDC1551 using phAE773 16 mc²8211 ΔargB mc²7477 unmarked using phAE280 17 mc²8392 ΔargB ΔmetA::hyg sacB Specialized transduction of mc²8211 using phAE783 18 mc²7901 ΔpanCD ΔleuCD ΔmetA **Pantothenate-leucine- methionine (PLA) auxotroph; isoniazid resistant 19 mc²7902 ΔpanCD ΔleuCD ΔargB **Pantothenate-leucine-arginine (PLA) auxotroph; rifampin resistant *Described in Tiwari, S. et al (2018) Arginine-deprivation-induced oxidative damage sterilizes Mycobacterium tuberculosis, Proc. Natl. Acad. Sci. USA, incorporated herein by reference. **Described in Vilchèze, C, et al Rational Design of Biosafety Level 2-Approved, Multidrug Resistant Strains of Mycobacterium tuberculosis through Nutrient Auxotrophy, mBio, 9 (3): e00938-18, pages 1-12.

Deprivation of L-Arginine and L-Methionine Sterilizes Mycobacterium tuberculosis.

Mycobacterium tuberculosis strain mc²8398 was cultured at 37° C. in Middlebrook 7H9 medium containing 10% OADC, 0.5% glycerol, and 0.05% tyloxapol, and further supplemented with L-arginine (1 mM) and L-methionine (50 μg/ml). Mid-log cultures were washed 5 times with PBS tyloxapol (PBST) and re-suspended in either arginine and methionine free media or arginine and methionine containing media (arginine 1 mM and L-methionine 50 μg/ml; mc²8398⁺). Samples were plated on arginine as well as methionine containing plates to determine CFU.

As shown in FIG. 3, the strain mc²8398 grew well in arginine and methionine containing media (mc²8398⁺) whereas there was substantially no growth in the arginine and methionine free media (mc²8398⁻) and by 30 days, there was substantially no bacteria remaining.

Strain Mc²8398 is Highly Attenuated in Immunocompromised SCID Mouse Model.

SCID mice (6/group) were infected with a high dose (10⁸ bacilli/animal) of strain mc²8398 or strain H37Rv. The percent survival of the mice over time is shown in FIG. 4A.

SCID mice (3/group) were infected with a high dose (10⁶ bacilli/animal) of strain mc²8398 or strain H37Rv, and the organ burden was determined by plating lung (FIG. 4B) Liver (FIG. 4C) and Spleen (FIG. 4D) on plates supplemented with both methionine and arginine.

The lung, liver, and spleen from infected mice, taken at different time points, were cultured on plates supplemented with arginine and methionine. As shown in FIGS. 4B to 4D, the Mtb ΔargBΔmetA was completely sterilized in the lung, liver, and spleen of the infected SCID mice by 120 days post-infection.

Strain Mc²8398 is Attenuated in in Lung, Liver and Spleen of Rag^(−/−) Mice Infected by Intravenous Route by 10⁸ Bacilli/Mice.

In house bred Rag−/− mice were infected intravenously with WT (H37Rv, CDC1551) and auxotrophic strains (mc²8392, mc²8398) at a very high dose of 10⁸ bacilli/animal. At the indicated time points, animals were sacrificed and organs (a) lung (b) spleen and (c) liver were plated on arginine and methionine containing plates to measure organ burden. The results are shown in FIGS. 5A to 5C.

Strain Mc²8398 is Highly Attenuated Compared to Other Auxotrophic Strains in Immunocompromised Rag^(−/−) Mice Model.

Rag−/− mice (4/group) were infected intravenously with WT (H37Rv, CDC1551) and auxotrophic strains (mc²8392, mc²8398, mc²7901, mc²7902) at a very high dose of 10⁸ bacilli/animal. At the indicated time points, animals were sacrificed and organs (a) lung (b) liver and (c) spleen were plated on arginine and methionine containing plates to measure organ burden. The results are shown in FIGS. 6A to 6C.

Strain Mc²8398 has Protective Efficacy Against Wild Type Mycobacterium tuberculosis Strain H37Rv by Different Routes of Immunization.

The strains and dosages in the experiment are provided in Table 2. C57BL/6 mice were immunized with PBS, BCG, or mc²8398 subcutaneously (SQ) or intravenously (iv) at Day 0 with 10⁶ bacilli/mouse and were boosted after 4 weeks with the indicated strains in Table 1, at a dose of 10⁶ bacilli/mouse. Four weeks following the booster immunization, the mice received a low dose aerosol challenge of ˜275 CFU/mouse of strain H37Rv. Organs were harvested at 2, 3, 8, 12, and 24 weeks post-challenge and plated to determine CFU burden in the lungs and spleen. FIG. 7 is an illustration showing the immunization and challenge schedule, and the results are shown in FIGS. 8A and 8B.

TABLE 2 Group Immunization (10⁶) Booster (10⁶) Challenge 1 Saline H37Rv, aerosol 2 BCG (SQ) H37Rv, aerosol 3 BCG (SQ) mc²8398 (SQ) H37Rv, aerosol 4 mc²8398(SQ) H37Rv, aerosol 5 mc²8398(SQ) mc²8398 (SQ) H37Rv, aerosol 6 mc²8398 (iv) H37Rv, aerosol

Protective Efficacy of Various Auxotrophic Mutants Against Clinical, Highly Virulent Mycobacterium tuberculosis Beijing Strain (HN878).

The strains and dosages used are provided in Table 3. C57BL/6 mice are immunized with PBS, BCG, or mc²8398 subcutaneously (SQ) or intravenously (iv) at Day 0 with 10⁶ bacilli/mouse and are boosted after 4 weeks with a same dose (10⁶ bacilli/mouse) of the same strain. Four weeks following the booster immunization, the mice receive a low dose aerosol challenge of ˜45 CFU/mouse of the virulent clinical isolate Beijing strain HN878. At 2, 5, 10, 16, and 24 weeks (W) post-challenge, organs are harvested and plated to determine CFU burden in the lungs and spleen. FIG. 9 is an illustration showing the immunization and challenge schedule.

TABLE 3 Group Immunization (10⁶) Booster (10⁶) Challenge 1 Saline HN878, aerosol 2 BCG (SQ) BCG (SQ) HN878, aerosol 3 mc²7901 (SQ) mc²7901 (SQ) HN878, aerosol 4 mc²7902 (SQ) mc²7902 (SQ) HN878, aerosol 5 mc²8392 (SQ) mc²8392 (SQ) HN878, aerosol 6 mc²8398 (SQ) mc²8398 (SQ) HN878, aerosol

Set forth below are some embodiments of the auxotrophic mycobacterium, the compositions, and the methods disclosed herein.

Embodiment 1: An auxotrophic mycobacterium comprising a mycobacterial genome in which (i) a gene encoding an enzyme essential in an arginine synthesis pathway has been fully or partially deleted and (ii) a gene encoding an enzyme essential in a methionine synthesis pathway has been fully or partially deleted.

Embodiment 2: The auxotrophic mycobacterium of Embodiment 1, which is incapable of synthesizing arginine and methionine.

Embodiment 3: The auxotrophic mycobacterium of Embodiment 1 or Embodiment 2, wherein the auxotrophic mycobacterium prior to the full or partial gene deletions of a gene encoding an enzyme essential in an arginine synthesis pathway and a gene encoding an enzyme essential in a methionine synthesis pathway is a Mycobacterium tuberculosis.

Embodiment 4: The auxotrophic mycobacterium of Embodiment 1 or Embodiment 2, wherein the auxotrophic mycobacterium prior to the full or partial gene deletions of a gene encoding an enzyme essential in an arginine synthesis pathway and a gene encoding an enzyme essential in a methionine synthesis pathway is a Mycobacterium bovis Bacillus Calmette-Guérin.

Embodiment 5: The auxotrophic mycobacterium of any one of Embodiments 1-4, wherein the gene encoding an enzyme essential in an arginine synthesis pathway is a mycobacterial argB gene or encodes a mycobacterial ArgB enzyme.

Embodiment 6: The auxotrophic mycobacterium of any one of Embodiments 1-5, wherein the gene encoding an enzyme essential in a methionine synthesis pathway is a mycobacterial metA gene or encodes a mycobacterial MetA enzyme.

Embodiment 7: The auxotrophic mycobacterium of any one of Embodiments 1-6, wherein the auxotrophic mycobacterium prior to the full or partial gene deletions of a gene encoding an enzyme essential in an arginine synthesis pathway and a gene encoding an enzyme essential in a methionine synthesis pathway is an H37Rv Mycobacterium tuberculosis.

Embodiment 8: A composition comprising the auxotrophic mycobacterium of any of Embodiments 1-7 and a carrier.

Embodiment 9: The composition of Embodiment 8 which is a vaccine.

Embodiment 10: The composition of Embodiment 8 or Embodiment 9, wherein the composition does not comprise arginine or methionine.

Embodiment 11: The composition of Embodiment 8 or Embodiment 9, wherein the composition comprises an amount of arginine and an amount of methionine.

Embodiment 12: A method of eliciting an immune response in a subject comprising administering to the subject the composition of any one of Embodiments 8-11 in an amount effective to elicit an immune response.

Embodiment 13: A method of vaccinating a subject comprising administering to the subject the composition of any one of Embodiments 8-11 in an amount effective to vaccinate a subject.

Embodiment 14: A method of treating a subject for tuberculosis comprising administering to the subject the composition of any one of Embodiments 8-11 in an amount effective to treat a subject.

Embodiment 15: The method of any one of Embodiments 12-14, wherein the subject has pulmonary tuberculosis.

Embodiment 16: The method of Embodiment 14, wherein the tuberculosis is pulmonary tuberculosis.

Embodiment 17: The method of any of Embodiments 12-14, wherein the subject has tuberculosis meningitis.

Embodiment 18: The method of Embodiment 14, wherein the tuberculosis is tuberculosis meningitis.

Embodiment 19: A method of treating a subject for a cancer comprising administering to the subject the composition of any one of Embodiments 8-11 in an amount effective to treat a subject.

Embodiment 20: The method of Embodiment 19, wherein the cancer is a genitourinary cancer.

Embodiment 21: The method of Embodiment 19 or Embodiment 20, wherein the cancer is a non-invasive bladder cancer.

Embodiment 22: The method of Embodiment 21, wherein the amount of the composition is administered into the bladder of the subject via a catheter.

Embodiment 23: The method of any one of Embodiments 19-22, wherein the subject is immunocompromised.

Embodiment 24: The method of any one of Embodiments 12-23, wherein the subject is human.

Embodiment 25: A method of determining the efficacy of a candidate tuberculosis vaccine, comprising: administering the candidate tuberculosis vaccine to an animal which has been infected with the auxotrophic mycobacterium of any of Embodiments 1-7, quantifying the amount of the auxotrophic mycobacterium in the animal at one or more time points subsequent to administering the candidate tuberculosis vaccine, and comparing the amount of auxotrophic mycobacterium quantified to a predetermined control amount, or to the amount of auxotrophic mycobacterium infected into the animal, so as to determine the efficacy of the candidate tuberculosis vaccine.

Embodiment 26: A method of determining the efficacy of a candidate small organic molecule tuberculosis treatment, comprising: administering the small organic molecule tuberculosis treatment to an animal which has been infected with the auxotrophic mycobacterium of any one of Embodiments 1-7, quantifying the amount of auxotrophic mycobacterium in the animal at one or more time points subsequent to administering the candidate tuberculosis vaccine, and comparing the amount of auxotrophic mycobacterium quantified to a predetermined control amount, or to the amount of auxotrophic mycobacterium infected into the animal, so as to determine the efficacy of the small organic molecule tuberculosis treatment.

Embodiment 27: The method of Embodiment 25 or Embodiment 26, wherein the mycobacterium further comprises a reporter gene insertion in the genome thereof and wherein the amount of auxotrophic mycobacterium in the animal at one or more time points is quantified by quantifying a reporter signal.

The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting. As used herein, the singular forms “a,” “an,” and “the” are intended to include the plural forms, including “at least one,” unless the content clearly indicates otherwise. “At least one” is not to be construed as limiting “a” or “an.” “Or” means “and/or.” As used herein, the term “and/or” includes any and all combinations of one or more of the associated listed items. It will be further understood that the terms “comprises” and/or “comprising,” or “includes” and/or “including” when used in this specification, specify the presence of stated features, regions, integers, steps, operations, elements, and/or components, but do not preclude the presence or addition of one or more other features, regions, integers, steps, operations, elements, components, and/or groups thereof.

Unless otherwise defined, all terms (including technical and scientific terms) used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. It will be further understood that terms, such as those defined in commonly used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of the relevant art and the present disclosure, and will not be interpreted in an idealized or overly formal sense unless expressly so defined herein.

Throughout this application various publications are referred to. Full citations for these references may be found at the end of the specification. The disclosures of these publications, and all patents, patent application publications and books referred to herein, are incorporated herein by reference in their entirety to more fully describe the art to which the subject invention pertains.

One skilled in the art will readily appreciate that the specific methods and results discussed hereinabove are merely illustrative of the invention as described more fully in the claims that follow thereafter.

REFERENCES

-   1. Berney, M, et al. (2015) Essential roles of methionine and     S-adenosylmethionine in the autarkic lifestyle of Mycobacterium     tuberculosis. Proc Natl Acad Sci USA 112:10008-10013. -   2. Minassian, A M, et al. (2012) A human challenge model for     Mycobacterium tuberculosis using Mycobacterium bovis bacille     Calmette-Guerin. J Infect Dis 205(7):1035-1042. -   3. N Thilothammal, et al. (1996) Does BCG vaccine prevent     tuberculous meningitis? Archives of Disease in Childhood 74. -   4. Alvaro, M (2017) BCG-A throwback from the stone age of vaccines     opened the path for bladder cancer immunotherapy. The Canadian     Journal of Urology 24(3):8788-8793. -   5. Gandhi, N M, Morales, A, & Lamm, D L (2013) Bacillus     Calmette-Guerin immunotherapy for genitourinary cancer. BJU Int     112(3):288-297. -   6. Ziegler J, et al. (2018) Disseminated Mycobacterium bovis     infection post-kidney transplant following remote intravesical BCG     therapy for bladder cancer. Transpl Infect Dis:e12931. -   7. Sheron M W, Holt S L, & Ingram C W (2017) Mycobacterium bovis     Cerebellar Abscess Following Treatment With Bacillus     Calmette-Guerin. J Pharm Pract 30(3):378-380. -   8. Marquez-Batalla S, Fraile-Villarejo E, Belhassen-Garcia M,     Gutierrez-Zubiaurre N, & Cordero-Sanchez M (2014) Disseminated     infection due to Mycobacterium bovis after intravesical BCG     instillation. World J Clin Cases 2(7):301-303. -   9. Serretta, V. (2015) Although rare, severe complications following     intravesical bacillus Calmette-Guerin treatment should not be     overlooked! Infect Dis (Lond) 47(10):732-733. -   10. Koya, M P, Simon M A, & Soloway M S (2006) Complications of     Intravesical Therapy for Urothelial Cancer of the Bladder. The     Journal of Urology 175(6):2004-2010. -   11. Jain, P., et al. (2014) Specialized transduction designed for     precise high-throughput unmarked deletions in Mycobacterium     tuberculosis. MBio 5(3):e01245-e14. -   12. Tiwari, S. et al, Arginine-deprivation-induced oxidative damage     sterilizes Mycobacterium tuberculosis, Proc. Natl. Acad. Sci. USA,     2018. -   13. Vilchèze, C, et al, (2018). Rational Design of Biosafety Level     2-Approved, Multidrug Resistant Strains of Mycobacterium     tuberculosis through Nutrient Auxotrophy, mBio 9 (3): e00938-18,     pages 1-12. 

1. An auxotrophic mycobacterium comprising a mycobacterial genome in which (i) a gene encoding an enzyme essential in an arginine synthesis pathway has been fully or partially deleted and (ii) a gene encoding an enzyme essential in a methionine synthesis pathway has been fully or partially deleted.
 2. The auxotrophic mycobacterium of claim 1, which is incapable of synthesizing arginine and methionine.
 3. The auxotrophic mycobacterium of claim 1, wherein the auxotrophic mycobacterium prior to the full or partial gene deletions of the gene encoding the enzyme essential in the arginine synthesis pathway and the gene encoding the enzyme essential in the methionine synthesis pathway is a Mycobacterium tuberculosis.
 4. The auxotrophic mycobacterium of claim 1, wherein the auxotrophic mycobacterium prior to the full or partial gene deletions of the gene encoding the enzyme essential in the arginine synthesis pathway and the gene encoding the enzyme essential in the methionine synthesis pathway is a Mycobacterium bovis Bacillus Calmette-Guérin.
 5. The auxotrophic mycobacterium of claim 1, wherein the gene encoding the enzyme essential in the arginine synthesis pathway is a mycobacterial argB gene or encodes a mycobacterial ArgB enzyme.
 6. The auxotrophic mycobacterium of claim 1, wherein the gene encoding the enzyme essential in the methionine synthesis pathway is a mycobacterial metA gene or encodes a mycobacterial MetA enzyme.
 7. The auxotrophic mycobacterium of claim 1, wherein the auxotrophic mycobacterium prior to the full or partial gene deletions of the gene encoding the enzyme essential in an arginine synthesis pathway and the gene encoding the enzyme essential in the methionine synthesis pathway is an H37Rv Mycobacterium tuberculosis.
 8. A composition comprising the auxotrophic mycobacterium of claim 1, and a carrier.
 9. The composition of claim 8, which is a vaccine.
 10. The composition of claim 8, wherein the composition does not comprise arginine or methionine.
 11. The composition of claim 8, wherein the composition comprises an amount of arginine and an amount of methionine.
 12. A method of eliciting an immune response in a subject comprising administering to the subject the composition of claim 8 in an amount effective to elicit an immune response.
 13. A method of vaccinating a subject comprising administering to the subject the composition of claim 8 in an amount effective to vaccinate a subject.
 14. A method of treating a subject for tuberculosis comprising administering to the subject the composition of claim 8 in an amount effective to treat a subject.
 15. The method of claim 12, wherein the subject has pulmonary tuberculosis.
 16. The method of claim 14, wherein the tuberculosis is pulmonary tuberculosis.
 17. The method of claim 12, wherein the subject has tuberculosis meningitis.
 18. The method of claim 14, wherein the tuberculosis is tuberculosis meningitis.
 19. A method of treating a subject for a cancer comprising administering to the subject the composition of claim 8 in an amount effective to treat a subject.
 20. The method of claim 19, wherein the cancer is a genitourinary cancer.
 21. The method of claim 19, wherein the cancer is a non-invasive bladder cancer.
 22. The method of claim 21, wherein the amount of the composition is administered into the bladder of the subject via a catheter.
 23. The method of claim 19, wherein the subject is immunocompromised.
 24. The method of claim 12, wherein the subject is human.
 25. A method of determining the efficacy of a candidate tuberculosis vaccine, comprising: administering the candidate tuberculosis vaccine to an animal which has been infected with the auxotrophic mycobacterium of claim 1, quantifying the amount of the auxotrophic mycobacterium in the animal at one or more time points subsequent to administering the candidate tuberculosis vaccine, and comparing the amount of auxotrophic mycobacterium quantified to a predetermined control amount, or to the amount of auxotrophic mycobacterium infected into the animal, so as to determine the efficacy of the candidate tuberculosis vaccine.
 26. A method of determining the efficacy of a candidate small organic molecule tuberculosis treatment, comprising: administering the small organic molecule tuberculosis treatment to an animal which has been infected with the auxotrophic mycobacterium of claim 1, quantifying the amount of auxotrophic mycobacterium in the animal at one or more time points subsequent to administering the candidate tuberculosis vaccine, and comparing the amount of auxotrophic mycobacterium quantified to a predetermined control amount, or to the amount of auxotrophic mycobacterium infected into the animal, so as to determine the efficacy of the small organic molecule tuberculosis treatment.
 27. The method of claim 25, wherein the mycobacterium further comprises a reporter gene insertion in the genome thereof and wherein the amount of auxotrophic mycobacterium in the animal at one or more time points is quantified by quantifying a reporter signal.
 28. A method of determining the efficacy of a candidate tuberculosis vaccine, comprising: administering the candidate tuberculosis vaccine to an animal which has been infected with the auxotrophic mycobacterium; quantifying an amount of the auxotrophic mycobacterium in the animal at one or more time points subsequent to administering the candidate tuberculosis vaccine, and comparing the amount of auxotrophic mycobacterium quantified to a predetermined control amount, or to the amount of auxotrophic mycobacterium infected into the animal, so as to determine the efficacy of the candidate tuberculosis vaccine, wherein the auxotrophic mycobacterium comprises a mycobacterial genome comprising: a full or partial deletion of a gene encoding an enzyme essential in a pantothenate synthesis pathway; a full or partial deletion of a gene encoding an enzyme essential in a leucine synthesis pathway; and a full or partial deletion of a gene encoding an enzyme essential in a methionine synthesis pathway or a full or partial deletion of a gene encoding an enzyme essential in an arginine synthesis pathway.
 29. A method of determining the efficacy of a candidate small organic molecule tuberculosis treatment, comprising: administering the small organic molecule tuberculosis treatment to an animal which has been infected with the auxotrophic mycobacterium, quantifying an amount of auxotrophic mycobacterium in the animal at one or more time points subsequent to administering the candidate tuberculosis vaccine, and comparing the amount of auxotrophic mycobacterium quantified to a predetermined control amount, or to the amount of auxotrophic mycobacterium infected into the animal, so as to determine the efficacy of the small organic molecule tuberculosis treatment, wherein the auxotrophic mycobacterium comprises a mycobacterial genome comprising: a full or partial deletion of a gene encoding an enzyme essential in a pantothenate synthesis pathway; a full or partial deletion of a gene encoding an enzyme essential in a leucine synthesis pathway; and a full or partial deletion of a gene encoding an enzyme essential in a methionine synthesis pathway or a full or partial deletion of a gene encoding an enzyme essential in an arginine synthesis pathway. 